Somewhat related to my other question Should raw Hibernate annotated POJO's be returned from the Data Access Layer, or Interfaces instead? , I am experienced in creation
Typically, you would want to isolate any persistence code to your DAO layer. So service layer should not even know about EntityManager. I think it's ok if DAO layer returns annotated pojos since they remain pojos still.
For the transaction management, I suggest that you look at Spring ORM. But if you choose not to use Spring or other AOP solution, you can always expose transaction related methods via your DAO so you call them from the service layer. Doing so will make your life much harder but the choice is yours...